Summary
|
Library
|
Total Reads in FASTQ
|
Pct Reads Passing Quality Filter
|
Pct CellLabel UMI Aligned Uniquely
|
|---|---|---|---|
| N22 TCR | 83,671,440 | 38.03% | 39.55% |
Putative Cells
85,988
|
Bioproduct Type
|
Aligned Reads By Type
|
Mean Reads per Cell
|
Mean Molecules per Cell
|
|---|---|---|---|
| mRNA | 3,875,539 | 32.62 | 29.79 |
| Sample Tags | 18,520 | 0.05 | - |
| VDJ TCR | 542,230 | 2.93 | 0.18 |
Graphs
No graphs available. (Usually due to too few or too many cells)
Sequence Quality
|
Library
|
Total Reads in FASTQ
|
Pct Read Pair Overlap
|
Pct Reads Too Short
|
Pct Reads Low Base Quality
|
Pct Reads High SNF
|
Pct Reads Filtered Out
|
Total Reads After Quality Filtering
|
|---|---|---|---|---|---|---|---|
| N22 TCR | 83,671,440 | 31.56% | 58.09% | 0.21% | 3.67% | 61.97% | 31,817,242 |
|
Library
|
Total Filtered Reads
|
Pct Q30 Bases in Filtered R2
|
Pct CellLabel UMI
|
Pct CellLabel UMI Aligned Uniquely
|
Pct Reads Useful
|
|---|---|---|---|---|---|
| N22 TCR | 31,817,242 | 62.94% | 48.18% | 39.55% | 13.94% |
Alignment Categories
|
Library
|
CellLabel UMI Reads
|
Annotated Transcriptome Pct
|
Introns Pct
|
Intergenic Regions Pct
|
Antisense Pct
|
Not Unique Pct
|
Ambiguous Pct
|
No Feature Pct
|
AbSeq Pct
|
Sample Tag Pct
|
VDJ TCR Pct
|
VDJ BCR Pct
|
Unaligned Pct
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| N22 TCR | 15,329,454 | 1.53% | 23.75% | 17.47% | 13.22% | 21.5% | 0.92% | 0.04% | 0% | 0.12% | 3.54% | 0% | 17.92% |
Reads and Molecules
|
Bioproduct Type
|
Aligned Reads By Type
|
Total Raw Molecules
|
Total RSEC Molecules
|
Mean Raw Sequencing Depth
|
Mean RSEC Sequencing Depth
|
Sequencing Saturation
|
|---|---|---|---|---|---|---|
| mRNA | 3,875,539 | 3,560,922 | 3,556,521 | 1.09 | 1.09 | 14.56 |
Cells
Putative Cells
Basic Algorithm Cells
|
Bioproduct Type
|
Pct Reads from Putative Cells
|
Mean Reads per Cell
|
Median Reads per Cell
|
Mean Molecules per Cell
|
Median Molecules per Cell
|
Mean Bioproducts per Cell
|
Median Bioproducts per Cell
|
Total Bioproducts Detected
|
|---|---|---|---|---|---|---|---|---|
| mRNA | 72.37% | 32.62 | 27 | 29.79 | 25 | 18.45 | 16 | 24,220 |
Sample Multiplexing
Valid Reads aligned to Sample Tags
Pct Reads from Putative Cells
|
Sample Tag
|
Sample Names
|
Raw Reads
|
Pct of Raw Reads
|
Cells Called
|
Pct of Putative Cells Called
|
Raw Reads in Called Cells
|
Mean Reads per Called Cell
|
|---|---|---|---|---|---|---|---|
| All_Tags | - | 18,520 | 100% | 85,988 | 100% | 3,894 | 0.05 |
| SampleTag01_flex | - | 1,658 | 8.95% | 1 | 0% | 220 | 220 |
| SampleTag02_flex | - | 3,814 | 20.59% | 72 | 0.08% | 890 | 12.36 |
| SampleTag03_flex | - | 1,550 | 8.37% | 0 | 0% | 0 | 0 |
| SampleTag04_flex | - | 1,652 | 8.92% | 25 | 0.03% | 284 | 11.36 |
| SampleTag05_flex | - | 2,789 | 15.06% | 49 | 0.06% | 588 | 12 |
| SampleTag06_flex | - | 3,841 | 20.74% | 64 | 0.07% | 1,306 | 20.41 |
| SampleTag07_flex | - | 1,363 | 7.36% | 16 | 0.02% | 168 | 10.5 |
| SampleTag08_flex | - | 1,848 | 9.98% | 30 | 0.03% | 438 | 14.6 |
| SampleTag09_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag10_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag11_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag12_flex | - | 2 | 0.01% | 0 | 0% | 0 | 0 |
| SampleTag13_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag14_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag15_flex | - | 1 | 0.01% | 0 | 0% | 0 | 0 |
| SampleTag16_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag17_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag18_flex | - | 1 | 0.01% | 0 | 0% | 0 | 0 |
| SampleTag19_flex | - | 1 | 0.01% | 0 | 0% | 0 | 0 |
| SampleTag20_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag21_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag22_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag23_flex | - | Not_Detected | - | - | - | - | - |
| SampleTag24_flex | - | Not_Detected | - | - | - | - | - |
| Multiplet | - | - | - | 0 | 0% | - | - |
| Undetermined | - | - | - | 85,731 | 99.7% | - | - |
VDJ
|
Chain Category
|
Reads Cellular Aligned to VDJ
|
Reads Contig Assembled
|
Reads VDJ Annotated
|
Reads Putative
|
Reads Corrected
|
Pct Reads Corrected
|
Mean Reads Corrected per Putative Cell
|
|
|---|---|---|---|---|---|---|---|---|
| TCR | 542,230 | 524,574 | 316,056 | 294,636 | 252,297 | 48.1% | 2.93 | |
| TCR Alpha | - | 41,853 | 19,590 | 18,409 | 14,838 | 35.45% | 0.17 | |
| TCR Beta | - | 461,099 | 289,144 | 269,286 | 231,120 | 50.12% | 2.69 | |
| TCR Delta | - | 2,309 | 781 | 752 | 721 | 31.23% | 0.01 | |
| TCR Gamma | - | 19,313 | 6,541 | 6,189 | 5,618 | 29.09% | 0.07 |
|
Chain Category
|
Mean Molecules Corrected per Putative Cell
|
Molecules VDJ Annotated
|
Molecules Corrected
|
Dominant Contigs Mean Nucleotide Length
|
Dominant Contigs Pct Full Length
|
Dominant Contigs Pct With CDR3
|
|
|---|---|---|---|---|---|---|---|
| TCR | 0.18 | 23,949 | 15,754 | 300 | 28.46% | 99.59% | |
| TCR Alpha | 0.03 | 3,991 | 2,866 | 347 | 42.46% | 99.28% | |
| TCR Beta | 0.14 | 19,059 | 12,167 | 290 | 25.55% | 99.77% | |
| TCR Delta | 0 | 259 | 231 | 309 | 26.03% | 94.52% | |
| TCR Gamma | 0.01 | 640 | 490 | 299 | 27.34% | 99.28% |
|
Cell Type
|
Number cells
|
TCR Paired Chains Any Pct
|
TCR Paired Chains Full Pct
|
|---|---|---|---|
| B | 74 | 16.22% | 8.11% |
| Dendritic | 14 | 0% | 0% |
| Monocyte classical | 84,080 | 0.31% | 0.12% |
| Monocyte nonclassical | 20 | 0% | 0% |
| Natural killer | 403 | 10.92% | 4.71% |
| T CD4 memory | 411 | 30.9% | 19.22% |
| T CD4 naive | 761 | 12.22% | 6.18% |
| T CD8 memory | 154 | 25.97% | 12.99% |
| T CD8 naive | 51 | 9.8% | 3.92% |
| T gamma delta | 20 | 35% | 5% |
Pipeline Inputs
Pipeline version: 2.0
Pipeline Start Time: Wed Jan 03 2024 14:06:20 GMT+0000 (Greenwich Mean Time)
AbSeq Reference:
- No value
- RhapRef_Human_WTA_2023-02.tar.gz
- No value
- No value
- N22_TCR_S1_R1_001.fastq.gz
- N22_TCR_S1_R2_001.fastq.gz
Multiplexing Settings
Sample Tags Version: flex
Tag Names:
VDJ Species Version: humanTCR
Enable Refined Putative Cell Calling: False
Exact Cell Count: No value
Expected Cell Count: No value
Putative Cell Call: mRNA
Metric Alerts
(Under development)
- May be due to short products in the library prep.
- Look for evidence of this in QC traces and contact customer support for suggestions on additional cleanups.
- May be due to short products in the library prep.
- Look for evidence of this in QC traces and contact customer support for suggestions on additional cleanups.
- May be due to poor sequencing or library quality, or incorrect reference panel.
- Check Q30 scores and QC traces, and confirm that the appropriate transcriptome reference and complete AbSeq reference was used.
- This can also occur if V1 and V2 beads are combined in a single library.
- May be due to poor sequencing or library quality; check QC traces and Illumina metrics to confirm sequencing was high quality.
- Ensure that correct reference panel was used.
- Ensure reads from long-read libraries have been trimmed before running the pipeline.
- May occur in experiments with low cell input. This can be addressed with additional cleanups for low cell input libraries (included in the protocol).
- Can also result from low cell viability or poor sequencing or library quality.
- This is expected if samples such as nuclei containing a high proportion of unprocessed transcripts are being run.